[2023-06-05 18:56:57,827] [INFO] DFAST_QC pipeline started.
[2023-06-05 18:56:57,829] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 18:56:57,829] [INFO] DQC Reference Directory: /var/lib/cwl/stgdd4edb1f-6402-4f61-b4f6-744b6fd46c32/dqc_reference
[2023-06-05 18:56:58,971] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 18:56:58,972] [INFO] Task started: Prodigal
[2023-06-05 18:56:58,972] [INFO] Running command: gunzip -c /var/lib/cwl/stg914b8074-08a7-487a-a1bb-3c7c602d651e/GCA_004144875.1_ASM414487v1_genomic.fna.gz | prodigal -d GCA_004144875.1_ASM414487v1_genomic.fna/cds.fna -a GCA_004144875.1_ASM414487v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 18:57:19,074] [INFO] Task succeeded: Prodigal
[2023-06-05 18:57:19,074] [INFO] Task started: HMMsearch
[2023-06-05 18:57:19,074] [INFO] Running command: hmmsearch --tblout GCA_004144875.1_ASM414487v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdd4edb1f-6402-4f61-b4f6-744b6fd46c32/dqc_reference/reference_markers.hmm GCA_004144875.1_ASM414487v1_genomic.fna/protein.faa > /dev/null
[2023-06-05 18:57:19,397] [INFO] Task succeeded: HMMsearch
[2023-06-05 18:57:19,398] [WARNING] Found 2/6 markers. [/var/lib/cwl/stg914b8074-08a7-487a-a1bb-3c7c602d651e/GCA_004144875.1_ASM414487v1_genomic.fna.gz]
[2023-06-05 18:57:19,465] [INFO] Query marker FASTA was written to GCA_004144875.1_ASM414487v1_genomic.fna/markers.fasta
[2023-06-05 18:57:19,466] [INFO] Task started: Blastn
[2023-06-05 18:57:19,466] [INFO] Running command: blastn -query GCA_004144875.1_ASM414487v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdd4edb1f-6402-4f61-b4f6-744b6fd46c32/dqc_reference/reference_markers.fasta -out GCA_004144875.1_ASM414487v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 18:57:20,130] [INFO] Task succeeded: Blastn
[2023-06-05 18:57:20,134] [INFO] Selected 31 target genomes.
[2023-06-05 18:57:20,134] [INFO] Target genome list was writen to GCA_004144875.1_ASM414487v1_genomic.fna/target_genomes.txt
[2023-06-05 18:57:20,152] [INFO] Task started: fastANI
[2023-06-05 18:57:20,152] [INFO] Running command: fastANI --query /var/lib/cwl/stg914b8074-08a7-487a-a1bb-3c7c602d651e/GCA_004144875.1_ASM414487v1_genomic.fna.gz --refList GCA_004144875.1_ASM414487v1_genomic.fna/target_genomes.txt --output GCA_004144875.1_ASM414487v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 18:57:44,661] [INFO] Task succeeded: fastANI
[2023-06-05 18:57:44,662] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdd4edb1f-6402-4f61-b4f6-744b6fd46c32/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 18:57:44,663] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdd4edb1f-6402-4f61-b4f6-744b6fd46c32/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 18:57:44,679] [INFO] Found 30 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 18:57:44,680] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-05 18:57:44,680] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Acidovorax radicis	strain=N35	GCA_000204195.2	758826	758826	type	True	78.4886	90	1138	95	below_threshold
Variovorax gossypii	strain=DSM 100435	GCA_003965815.1	1679495	1679495	type	True	78.4705	94	1138	95	below_threshold
Variovorax boronicumulans	strain=NBRC 103145	GCA_001591345.1	436515	436515	type	True	78.2582	131	1138	95	below_threshold
Variovorax paradoxus	strain=NBRC 15149	GCA_001591365.1	34073	34073	suspected-type	True	78.1618	121	1138	95	below_threshold
Acidovorax wautersii	strain=DSM 27981	GCA_900113035.1	1177982	1177982	type	True	78.0383	104	1138	95	below_threshold
Variovorax guangxiensis	strain=DSM 27352	GCA_003952165.1	1775474	1775474	type	True	78.0321	121	1138	95	below_threshold
Acidovorax oryzae	strain=ATCC 19882	GCA_000687165.1	862720	862720	type	True	77.9927	86	1138	95	below_threshold
Bordetella bronchiseptica	strain=CCUG 219	GCA_021391275.1	518	518	suspected-type	True	77.9131	133	1138	95	below_threshold
Acidovorax kalamii	strain=KNDSW-TSA6	GCA_002245625.1	2004485	2004485	type	True	77.8836	89	1138	95	below_threshold
Ramlibacter tataouinensis	strain=TTB310	GCA_000215705.1	94132	94132	type	True	77.8548	89	1138	95	below_threshold
Acidovorax soli	strain=DSM 25157	GCA_900107605.1	592050	592050	type	True	77.8393	71	1138	95	below_threshold
Acidovorax citrulli	strain=DSM 17060	GCA_900100305.1	80869	80869	type	True	77.8363	82	1138	95	below_threshold
Acidovorax facilis	strain=DSM 649	GCA_023913775.1	12917	12917	type	True	77.7627	87	1138	95	below_threshold
Acidovorax anthurii	strain=CFPB 3232	GCA_003269065.1	78229	78229	type	True	77.6884	87	1138	95	below_threshold
Achromobacter deleyi	strain=LMG 3458	GCA_902859705.1	1353891	1353891	type	True	77.6456	164	1138	95	below_threshold
Achromobacter insuavis	strain=LMG 26845	GCA_902859645.1	1287735	1287735	type	True	77.5577	166	1138	95	below_threshold
Acidovorax temperans	strain=DSM 7270	GCA_006716905.1	80878	80878	type	True	77.4485	74	1138	95	below_threshold
Achromobacter pulmonis	strain=LMG 26696	GCA_902859765.1	1389932	1389932	type	True	77.4375	152	1138	95	below_threshold
Acidovorax delafieldii	strain=DSM 64	GCA_007993815.1	47920	47920	type	True	77.4171	83	1138	95	below_threshold
Achromobacter xylosoxidans	strain=PartM-Axylosoxidans-RM8376	GCA_022870085.1	85698	85698	type	True	77.3788	175	1138	95	below_threshold
Achromobacter xylosoxidans	strain=FDAARGOS_789	GCA_013343135.1	85698	85698	type	True	77.3449	176	1138	95	below_threshold
Achromobacter xylosoxidans	strain=NCTC10807	GCA_001457475.1	85698	85698	type	True	77.3303	176	1138	95	below_threshold
Achromobacter xylosoxidans	strain=NBRC 15126	GCA_001598595.1	85698	85698	type	True	77.2896	175	1138	95	below_threshold
Achromobacter piechaudii	strain=LMG 1873	GCA_902859685.1	72556	72556	type	True	77.2294	143	1138	95	below_threshold
Bordetella flabilis	strain=AU10664	GCA_001676725.1	463014	463014	type	True	77.1694	125	1138	95	below_threshold
Achromobacter piechaudii	strain=NBRC 102461	GCA_001571245.1	72556	72556	type	True	77.1694	143	1138	95	below_threshold
Achromobacter insolitus	strain=NCTC 13520	GCA_024168865.1	217204	217204	type	True	76.925	150	1138	95	below_threshold
Massilia agilis	strain=JCM 31605	GCA_024756255.1	1811226	1811226	type	True	76.9198	59	1138	95	below_threshold
Ralstonia pseudosolanacearum	strain=LMG 9673	GCA_919586305.1	1310165	1310165	type	True	76.4475	73	1138	95	below_threshold
Massilia agri	strain=JCM 31661	GCA_024753255.1	1886785	1886785	type	True	76.161	70	1138	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-05 18:57:44,682] [INFO] DFAST Taxonomy check result was written to GCA_004144875.1_ASM414487v1_genomic.fna/tc_result.tsv
[2023-06-05 18:57:44,682] [INFO] ===== Taxonomy check completed =====
[2023-06-05 18:57:44,682] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 18:57:44,682] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdd4edb1f-6402-4f61-b4f6-744b6fd46c32/dqc_reference/checkm_data
[2023-06-05 18:57:44,683] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 18:57:44,762] [INFO] Task started: CheckM
[2023-06-05 18:57:44,762] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_004144875.1_ASM414487v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_004144875.1_ASM414487v1_genomic.fna/checkm_input GCA_004144875.1_ASM414487v1_genomic.fna/checkm_result
[2023-06-05 18:58:42,162] [INFO] Task succeeded: CheckM
[2023-06-05 18:58:42,163] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 61.50%
Contamintation: 17.05%
Strain heterogeneity: 33.33%
--------------------------------------------------------------------------------
[2023-06-05 18:58:42,187] [INFO] ===== Completeness check finished =====
[2023-06-05 18:58:42,187] [INFO] ===== Start GTDB Search =====
[2023-06-05 18:58:42,189] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_004144875.1_ASM414487v1_genomic.fna/markers.fasta)
[2023-06-05 18:58:42,189] [INFO] Task started: Blastn
[2023-06-05 18:58:42,189] [INFO] Running command: blastn -query GCA_004144875.1_ASM414487v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdd4edb1f-6402-4f61-b4f6-744b6fd46c32/dqc_reference/reference_markers_gtdb.fasta -out GCA_004144875.1_ASM414487v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 18:58:43,304] [INFO] Task succeeded: Blastn
[2023-06-05 18:58:43,307] [INFO] Selected 32 target genomes.
[2023-06-05 18:58:43,308] [INFO] Target genome list was writen to GCA_004144875.1_ASM414487v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 18:58:43,460] [INFO] Task started: fastANI
[2023-06-05 18:58:43,460] [INFO] Running command: fastANI --query /var/lib/cwl/stg914b8074-08a7-487a-a1bb-3c7c602d651e/GCA_004144875.1_ASM414487v1_genomic.fna.gz --refList GCA_004144875.1_ASM414487v1_genomic.fna/target_genomes_gtdb.txt --output GCA_004144875.1_ASM414487v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 18:59:11,235] [INFO] Task succeeded: fastANI
[2023-06-05 18:59:11,254] [INFO] Found 32 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-05 18:59:11,254] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCA_018241185.1	s__ALPHA2B sp018241185	79.0608	92	1138	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__ALPHA2B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001424425.1	s__Acidovorax sp001424425	78.9272	112	1138	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	99.93	99.87	0.98	0.97	3	-
GCF_003671765.1	s__ALPHA2B sp003671765	78.7804	114	1138	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__ALPHA2B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_901875635.1	s__ALPHA2B sp901875635	78.4154	103	1138	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__ALPHA2B	95.0	99.68	99.68	0.89	0.89	2	-
GCF_019219095.1	s__Acidovorax sp019219095	78.2599	86	1138	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005503065.1	s__ALPHA2B sp005503065	78.1268	122	1138	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__ALPHA2B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900113035.1	s__Acidovorax_A wautersii	78.1073	102	1138	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019218755.1	s__Acidovorax sp019218755	78.0542	92	1138	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	98.86	98.86	0.92	0.91	3	-
GCF_013408765.1	s__Acidovorax sp013408765	77.9037	103	1138	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003053545.1	s__Acidovorax sp003053545	77.8051	112	1138	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	98.66	97.32	0.95	0.90	3	-
GCA_018828125.1	s__Acidovorax sp018828125	77.7776	74	1138	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	99.50	98.69	0.98	0.93	11	-
GCF_016806145.1	s__Variovorax sp900115375	77.7249	140	1138	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Variovorax	95.0	96.08	95.68	0.83	0.79	13	-
GCF_902859705.1	s__Achromobacter deleyi	77.6456	164	1138	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	98.99	97.40	0.95	0.91	5	-
GCF_014207955.1	s__Acidovorax soli_A	77.6166	122	1138	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003208485.1	s__Acidovorax sp003208485	77.5809	111	1138	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902859695.1	s__Achromobacter ruhlandii	77.5783	173	1138	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0063	98.29	97.95	0.91	0.85	19	-
GCF_902859645.1	s__Achromobacter insuavis	77.5577	166	1138	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.6014	99.48	98.86	0.95	0.90	7	-
GCF_002885955.2	s__Achromobacter pulmonis_A	77.459	155	1138	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	98.97	98.79	0.92	0.89	3	-
GCF_902859765.1	s__Achromobacter pulmonis	77.4375	152	1138	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	99.40	99.40	0.96	0.96	2	-
GCF_000657795.2	s__Bordetella pseudohinzii	77.4247	146	1138	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Bordetella	95.0	99.97	99.86	0.99	0.98	8	-
GCF_002902905.1	s__Achromobacter sp002902905	77.4125	159	1138	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	96.15	96.15	0.87	0.87	2	-
GCF_001428665.1	s__Acidovorax sp001428665	77.3895	113	1138	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	97.34	97.34	0.92	0.92	2	-
GCF_016127315.1	s__Achromobacter insuavis_A	77.3743	170	1138	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.6014	97.14	97.13	0.90	0.90	4	-
GCF_000165835.1	s__Achromobacter xylosoxidans_B	77.3478	146	1138	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	96.34	96.34	0.92	0.92	2	-
GCF_001457475.1	s__Achromobacter xylosoxidans	77.3455	175	1138	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	98.72	96.70	0.93	0.87	75	-
GCF_017356245.1	s__Bordetella_A petrii_D	77.3392	144	1138	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Bordetella_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002261345.1	s__Bordetella_A sp002261345	77.2445	144	1138	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Bordetella_A	95.0	99.26	99.26	0.94	0.94	2	-
GCF_001270295.1	s__Achromobacter sp001270295	77.2112	136	1138	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001676725.1	s__Bordetella_C flabilis	77.1694	125	1138	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Bordetella_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019218885.1	s__Bordetella_A sp019218885	77.122	138	1138	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Bordetella_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017745595.1	s__Bordetella_A petrii_C	76.9993	143	1138	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Bordetella_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000067205.1	s__Bordetella_A petrii	76.9394	136	1138	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Bordetella_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-05 18:59:11,256] [INFO] GTDB search result was written to GCA_004144875.1_ASM414487v1_genomic.fna/result_gtdb.tsv
[2023-06-05 18:59:11,257] [INFO] ===== GTDB Search completed =====
[2023-06-05 18:59:11,261] [INFO] DFAST_QC result json was written to GCA_004144875.1_ASM414487v1_genomic.fna/dqc_result.json
[2023-06-05 18:59:11,262] [INFO] DFAST_QC completed!
[2023-06-05 18:59:11,262] [INFO] Total running time: 0h2m13s